HEADER DNA BINDING PROTEIN 19-DEC-17 6FBD TITLE KLENTAQ DNA POLYMERASE PROCESSING A MODIFIED PRIMER - BEARING THE TITLE 2 MODIFICATION UPSTREAM AT THE SECOND PRIMER NUCLEOTIDE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TAQ POLYMERASE 1; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*AP*(OH3)P*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'- COMPND 13 D(P*AP*AP*AP*CP*GP*GP*TP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POLA, POL1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, MODIFIED NUCLEOTIDES, KLENTAQ, KLENTAQ DNA KEYWDS 2 POLYMERASE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.M.KROPP,K.DIEDERICHS,A.MARX REVDAT 4 08-MAY-24 6FBD 1 LINK REVDAT 3 14-AUG-19 6FBD 1 COMPND REMARK REVDAT 2 10-OCT-18 6FBD 1 COMPND JRNL REVDAT 1 26-SEP-18 6FBD 0 JRNL AUTH H.M.KROPP,S.L.DURR,C.PETER,K.DIEDERICHS,A.MARX JRNL TITL SNAPSHOTS OF A MODIFIED NUCLEOTIDE MOVING THROUGH THE JRNL TITL 2 CONFINES OF A DNA POLYMERASE. JRNL REF PROC. NATL. ACAD. SCI. V. 115 9992 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 30224478 JRNL DOI 10.1073/PNAS.1811518115 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12RC1_2815: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 72023 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 3616 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.0939 - 6.2136 1.00 2613 152 0.1703 0.1770 REMARK 3 2 6.2136 - 4.9336 1.00 2630 149 0.1653 0.2018 REMARK 3 3 4.9336 - 4.3105 1.00 2646 119 0.1439 0.1804 REMARK 3 4 4.3105 - 3.9166 1.00 2591 170 0.1606 0.1979 REMARK 3 5 3.9166 - 3.6360 1.00 2605 169 0.1749 0.2041 REMARK 3 6 3.6360 - 3.4217 1.00 2626 147 0.1841 0.1999 REMARK 3 7 3.4217 - 3.2504 1.00 2615 142 0.2029 0.2592 REMARK 3 8 3.2504 - 3.1089 1.00 2640 145 0.2256 0.2528 REMARK 3 9 3.1089 - 2.9892 1.00 2653 111 0.2335 0.2975 REMARK 3 10 2.9892 - 2.8861 1.00 2633 164 0.2390 0.3150 REMARK 3 11 2.8861 - 2.7959 1.00 2578 158 0.2438 0.2800 REMARK 3 12 2.7959 - 2.7160 1.00 2688 127 0.2219 0.2668 REMARK 3 13 2.7160 - 2.6445 1.00 2567 141 0.2283 0.2334 REMARK 3 14 2.6445 - 2.5799 1.00 2682 156 0.2336 0.2846 REMARK 3 15 2.5799 - 2.5213 1.00 2600 160 0.2272 0.2717 REMARK 3 16 2.5213 - 2.4676 1.00 2620 132 0.2301 0.2942 REMARK 3 17 2.4676 - 2.4183 1.00 2618 132 0.2348 0.2411 REMARK 3 18 2.4183 - 2.3727 1.00 2689 104 0.2429 0.3328 REMARK 3 19 2.3727 - 2.3303 1.00 2659 121 0.2501 0.2754 REMARK 3 20 2.3303 - 2.2908 1.00 2576 136 0.2492 0.3285 REMARK 3 21 2.2908 - 2.2538 1.00 2674 145 0.2594 0.2793 REMARK 3 22 2.2538 - 2.2192 1.00 2676 112 0.2676 0.3180 REMARK 3 23 2.2192 - 2.1865 1.00 2630 142 0.2703 0.3570 REMARK 3 24 2.1865 - 2.1557 1.00 2633 116 0.2697 0.2652 REMARK 3 25 2.1557 - 2.1266 1.00 2639 130 0.2932 0.3561 REMARK 3 26 2.1266 - 2.0990 0.99 2626 136 0.3003 0.3610 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 4944 REMARK 3 ANGLE : 0.575 6801 REMARK 3 CHIRALITY : 0.040 762 REMARK 3 PLANARITY : 0.003 820 REMARK 3 DIHEDRAL : 16.674 2886 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 294 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.4901 -40.6866 -18.2404 REMARK 3 T TENSOR REMARK 3 T11: 0.3668 T22: 0.3822 REMARK 3 T33: 0.5645 T12: -0.1101 REMARK 3 T13: 0.0835 T23: -0.0275 REMARK 3 L TENSOR REMARK 3 L11: 1.5650 L22: 1.1722 REMARK 3 L33: 1.6469 L12: -0.3713 REMARK 3 L13: -0.0441 L23: 0.1439 REMARK 3 S TENSOR REMARK 3 S11: -0.0246 S12: -0.0355 S13: -0.6454 REMARK 3 S21: -0.2187 S22: 0.0594 S23: -0.3164 REMARK 3 S31: 0.2000 S32: -0.0307 S33: -0.0262 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 453 THROUGH 562 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.1195 -9.0599 6.6075 REMARK 3 T TENSOR REMARK 3 T11: 0.5980 T22: 0.2665 REMARK 3 T33: 0.3737 T12: -0.0176 REMARK 3 T13: 0.0305 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 1.8896 L22: 2.0512 REMARK 3 L33: 2.3798 L12: 1.0690 REMARK 3 L13: -0.6845 L23: -0.2347 REMARK 3 S TENSOR REMARK 3 S11: 0.2415 S12: -0.2281 S13: 0.3132 REMARK 3 S21: 0.2394 S22: -0.2041 S23: 0.1208 REMARK 3 S31: -0.9474 S32: 0.1741 S33: -0.0407 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 563 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.4212 -20.6178 -11.6829 REMARK 3 T TENSOR REMARK 3 T11: 0.4201 T22: 0.6192 REMARK 3 T33: 0.3069 T12: 0.1470 REMARK 3 T13: 0.0108 T23: 0.0609 REMARK 3 L TENSOR REMARK 3 L11: 1.5883 L22: 1.7078 REMARK 3 L33: 2.5204 L12: 0.4674 REMARK 3 L13: 0.1634 L23: -0.8574 REMARK 3 S TENSOR REMARK 3 S11: -0.1231 S12: -0.1097 S13: 0.0826 REMARK 3 S21: 0.0184 S22: 0.2904 S23: 0.2728 REMARK 3 S31: -0.6414 S32: -0.9527 S33: -0.1398 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.8206 -22.9043 4.0249 REMARK 3 T TENSOR REMARK 3 T11: 0.3357 T22: 0.3976 REMARK 3 T33: 0.4171 T12: 0.0850 REMARK 3 T13: 0.0373 T23: 0.0732 REMARK 3 L TENSOR REMARK 3 L11: 1.6660 L22: 1.6724 REMARK 3 L33: 1.5106 L12: 1.0112 REMARK 3 L13: 0.0265 L23: -0.8986 REMARK 3 S TENSOR REMARK 3 S11: 0.0652 S12: 0.3997 S13: -0.3887 REMARK 3 S21: 0.2081 S22: -0.3331 S23: -0.1546 REMARK 3 S31: -0.3115 S32: 0.3087 S33: 0.2436 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 204 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.3509 -24.0069 5.0893 REMARK 3 T TENSOR REMARK 3 T11: 0.3230 T22: 0.4319 REMARK 3 T33: 0.3445 T12: 0.0488 REMARK 3 T13: 0.0232 T23: 0.0698 REMARK 3 L TENSOR REMARK 3 L11: 0.6318 L22: 1.9402 REMARK 3 L33: 1.3660 L12: 0.3740 REMARK 3 L13: -0.2596 L23: 0.8295 REMARK 3 S TENSOR REMARK 3 S11: -0.1088 S12: -0.1275 S13: -0.2156 REMARK 3 S21: 0.1951 S22: 0.1851 S23: -0.1962 REMARK 3 S31: -0.0820 S32: -0.1045 S33: -0.1083 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FBD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007857. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72040 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.099 REMARK 200 RESOLUTION RANGE LOW (A) : 47.616 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.180 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.940 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16 % PEG 4000, 0.1 M HEPES, 25 MM REMARK 280 MANGANESE(II) CHLORIDE, 0.1 M SODIUM ACETATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.38833 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.77667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.77667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.38833 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 292 REMARK 465 ALA A 293 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 294 CG CD1 CD2 REMARK 470 GLU A 295 CG CD OE1 OE2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 ARG A 392 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 411 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 ARG A 469 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 473 CG CD OE1 OE2 REMARK 470 ILE A 503 CG1 CG2 CD1 REMARK 470 GLU A 524 CG CD OE1 OE2 REMARK 470 ARG A 630 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 634 CG CD OE1 OE2 REMARK 470 SER A 644 OG REMARK 470 TRP A 645 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 645 CZ3 CH2 REMARK 470 VAL A 649 CG1 CG2 REMARK 470 GLU A 652 CG CD OE1 OE2 REMARK 470 HIS A 676 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 680 CG CD OE1 NE2 REMARK 470 GLU A 687 CG CD OE1 OE2 REMARK 470 GLU A 688 CG CD OE1 OE2 REMARK 470 ARG A 695 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 697 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 702 CG CD CE NZ REMARK 470 VAL A 703 CG1 CG2 REMARK 470 ARG A 704 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 709 CG CD CE NZ REMARK 470 GLU A 713 CG CD OE1 OE2 REMARK 470 LYS A 793 CG CD CE NZ REMARK 470 GLU A 794 CG CD OE1 OE2 REMARK 470 ARG A 795 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 801 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 818 CG CD OE1 OE2 REMARK 470 GLU A 825 CG CD OE1 OE2 REMARK 470 GLU A 832 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O5' DG C 214 O HOH C 401 2.13 REMARK 500 O HOH C 416 O HOH C 429 2.16 REMARK 500 NH2 ARG A 523 OE1 GLU A 530 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 D4B B 111 O3' - P - OP2 ANGL. DEV. = 19.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 328 144.30 -172.01 REMARK 500 ASP A 381 111.52 -160.85 REMARK 500 THR A 399 -163.39 -110.20 REMARK 500 GLU A 421 108.17 -57.11 REMARK 500 VAL A 433 -69.73 -131.16 REMARK 500 ASP A 496 -69.29 -95.87 REMARK 500 TYR A 545 -57.68 -128.04 REMARK 500 VAL A 586 -19.91 -162.84 REMARK 500 ASP A 625 107.84 -56.53 REMARK 500 ARG A 651 -80.78 14.91 REMARK 500 LEU A 682 -29.74 70.86 REMARK 500 HIS A 784 -64.87 70.74 REMARK 500 TYR A 811 92.65 -164.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 901 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 785 OD1 101.7 REMARK 620 3 GLU A 786 OE1 69.7 112.7 REMARK 620 4 XG4 A 903 O1A 102.7 93.3 153.8 REMARK 620 5 HOH A1003 O 91.3 94.7 26.2 162.1 REMARK 620 6 HOH A1012 O 90.3 167.7 74.0 81.2 87.7 REMARK 620 7 DC B 112 O3' 167.8 67.2 109.1 83.5 84.9 101.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 902 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 75.7 REMARK 620 3 ASP A 785 OD2 81.0 91.3 REMARK 620 4 XG4 A 903 O1A 92.4 165.7 78.8 REMARK 620 5 XG4 A 903 O1B 173.5 99.5 94.7 91.6 REMARK 620 6 XG4 A 903 O3G 91.0 91.9 170.4 96.3 93.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 304 O REMARK 620 2 HOH B 305 O 91.9 REMARK 620 3 HOH B 311 O 86.4 90.3 REMARK 620 4 HOH B 313 O 163.0 96.7 79.0 REMARK 620 5 HOH B 314 O 80.8 171.0 84.1 89.0 REMARK 620 6 HOH C 430 O 87.7 90.2 174.1 106.8 94.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 416 O REMARK 620 2 HOH C 422 O 164.9 REMARK 620 3 HOH C 425 O 69.2 95.7 REMARK 620 4 HOH C 426 O 97.9 97.1 166.8 REMARK 620 5 HOH C 432 O 97.9 79.6 85.6 93.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XG4 A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 302 DBREF 6FBD A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 6FBD B 101 112 PDB 6FBD 6FBD 101 112 DBREF 6FBD C 201 216 PDB 6FBD 6FBD 201 216 SEQADV 6FBD MET A 292 UNP P19821 INITIATING METHIONINE SEQRES 1 A 541 MET ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY SEQRES 2 A 541 ALA PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET SEQRES 3 A 541 TRP ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY SEQRES 4 A 541 ARG VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG SEQRES 5 A 541 ASP LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SEQRES 6 A 541 SER VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO SEQRES 7 A 541 GLY ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SEQRES 8 A 541 SER ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY SEQRES 9 A 541 GLY GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SEQRES 10 A 541 SER GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU SEQRES 11 A 541 GLY GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU SEQRES 12 A 541 ARG PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR SEQRES 13 A 541 GLY VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER SEQRES 14 A 541 LEU GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU SEQRES 15 A 541 VAL PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER SEQRES 16 A 541 ARG ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY SEQRES 17 A 541 LEU PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SEQRES 18 A 541 SER THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA SEQRES 19 A 541 HIS PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU SEQRES 20 A 541 THR LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP SEQRES 21 A 541 LEU ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE SEQRES 22 A 541 ASN GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER SEQRES 23 A 541 ASP PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU SEQRES 24 A 541 GLY GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY SEQRES 25 A 541 TRP LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU SEQRES 26 A 541 ARG VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE SEQRES 27 A 541 ARG VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR SEQRES 28 A 541 ALA SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP SEQRES 29 A 541 PRO LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY SEQRES 30 A 541 VAL LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU SEQRES 31 A 541 LEU ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU SEQRES 32 A 541 ARG TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE SEQRES 33 A 541 GLU LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL SEQRES 34 A 541 GLU THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU SEQRES 35 A 541 GLU ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG SEQRES 36 A 541 MET ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP SEQRES 37 A 541 LEU MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU SEQRES 38 A 541 GLU GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP SEQRES 39 A 541 GLU LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA SEQRES 40 A 541 VAL ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR SEQRES 41 A 541 PRO LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY SEQRES 42 A 541 GLU ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DA D4B DC SEQRES 1 C 16 DA DA DA DC DG DG DT DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC HET D4B B 111 44 HET MN A 901 1 HET MN A 902 1 HET XG4 A 903 44 HET MG B 201 1 HET GOL C 301 14 HET MG C 302 1 HETNAM D4B [(2~{R},3~{S},5~{R})-5-[4-AZANYL-5-[2-(4- HETNAM 2 D4B ETHYNYLPHENYL)ETHYNYL]-2-OXIDANYLIDENE-PYRIMIDIN-1- HETNAM 3 D4B YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 D4B C19 H18 N3 O7 P FORMUL 4 MN 2(MN 2+) FORMUL 6 XG4 C10 H17 N6 O12 P3 FORMUL 7 MG 2(MG 2+) FORMUL 8 GOL C3 H8 O3 FORMUL 10 HOH *164(H2 O) HELIX 1 AA1 GLU A 337 ARG A 343 1 7 HELIX 2 AA2 LEU A 352 GLU A 363 1 12 HELIX 3 AA3 ASP A 372 ASP A 381 1 10 HELIX 4 AA4 THR A 386 GLY A 395 1 10 HELIX 5 AA5 GLU A 401 GLU A 421 1 21 HELIX 6 AA6 GLU A 423 VAL A 433 1 11 HELIX 7 AA7 VAL A 433 GLY A 448 1 16 HELIX 8 AA8 ASP A 452 GLY A 479 1 28 HELIX 9 AA9 SER A 486 ASP A 496 1 11 HELIX 10 AB1 SER A 515 LEU A 522 1 8 HELIX 11 AB2 HIS A 526 TYR A 545 1 20 HELIX 12 AB3 PRO A 548 ILE A 553 5 6 HELIX 13 AB4 THR A 588 ARG A 596 1 9 HELIX 14 AB5 GLN A 613 GLY A 624 1 12 HELIX 15 AB6 ASP A 625 GLU A 634 1 10 HELIX 16 AB7 ASP A 637 GLY A 648 1 12 HELIX 17 AB8 PRO A 650 VAL A 654 5 5 HELIX 18 AB9 ASP A 655 TYR A 671 1 17 HELIX 19 AC1 SER A 674 GLU A 681 1 8 HELIX 20 AC2 LEU A 682 ILE A 684 5 3 HELIX 21 AC3 PRO A 685 PHE A 700 1 16 HELIX 22 AC4 PRO A 701 GLY A 718 1 18 HELIX 23 AC5 PRO A 731 ALA A 735 5 5 HELIX 24 AC6 VAL A 737 MET A 775 1 39 HELIX 25 AC7 ARG A 795 GLY A 809 1 15 HELIX 26 AC8 ASP A 826 LYS A 831 1 6 SHEET 1 AA1 4 GLU A 295 ALA A 297 0 SHEET 2 AA1 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 AA1 4 LEU A 321 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 AA1 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 SHEET 1 AA2 2 ARG A 450 LEU A 451 0 SHEET 2 AA2 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 AA3 2 ARG A 563 ASN A 565 0 SHEET 2 AA3 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 AA4 4 ARG A 778 GLN A 782 0 SHEET 2 AA4 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 AA4 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 AA4 4 VAL A 819 GLY A 824 -1 O GLU A 820 N ASP A 610 SHEET 1 AA5 2 TYR A 719 GLU A 721 0 SHEET 2 AA5 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DA B 110 P D4B B 111 1555 1555 1.60 LINK O3' D4B B 111 P DC B 112 1555 1555 1.60 LINK OD2 ASP A 610 MN MN A 901 1555 1555 2.14 LINK OD1 ASP A 610 MN MN A 902 1555 1555 2.14 LINK O TYR A 611 MN MN A 902 1555 1555 2.09 LINK OD1 ASP A 785 MN MN A 901 1555 1555 2.13 LINK OD2 ASP A 785 MN MN A 902 1555 1555 2.13 LINK OE1AGLU A 786 MN MN A 901 1555 1555 2.15 LINK MN MN A 901 O1A XG4 A 903 1555 1555 2.11 LINK MN MN A 901 O BHOH A1003 1555 1555 2.13 LINK MN MN A 901 O HOH A1012 1555 1555 2.03 LINK MN MN A 901 O3' DC B 112 1555 1555 2.15 LINK MN MN A 902 O1A XG4 A 903 1555 1555 2.34 LINK MN MN A 902 O1B XG4 A 903 1555 1555 2.18 LINK MN MN A 902 O3G XG4 A 903 1555 1555 2.15 LINK MG MG B 201 O HOH B 304 1555 1555 2.26 LINK MG MG B 201 O HOH B 305 1555 1555 2.07 LINK MG MG B 201 O HOH B 311 1555 1555 2.05 LINK MG MG B 201 O HOH B 313 1555 1555 2.10 LINK MG MG B 201 O HOH B 314 1555 1555 2.17 LINK MG MG B 201 O HOH C 430 1555 1555 2.11 LINK MG MG C 302 O HOH C 416 1555 1555 2.34 LINK MG MG C 302 O HOH C 422 1555 1555 2.21 LINK MG MG C 302 O HOH C 425 1555 1555 2.20 LINK MG MG C 302 O HOH C 426 1555 1555 2.03 LINK MG MG C 302 O HOH C 432 1555 1555 2.33 CISPEP 1 TRP A 299 PRO A 300 0 2.11 CISPEP 2 ASP A 578 PRO A 579 0 -0.26 SITE 1 AC1 8 ASP A 610 ASP A 785 GLU A 786 MN A 902 SITE 2 AC1 8 XG4 A 903 HOH A1003 HOH A1012 DC B 112 SITE 1 AC2 5 ASP A 610 TYR A 611 ASP A 785 MN A 901 SITE 2 AC2 5 XG4 A 903 SITE 1 AC3 21 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC3 21 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC3 21 ARG A 659 LYS A 663 PHE A 667 TYR A 671 SITE 4 AC3 21 ASP A 785 MN A 901 MN A 902 HOH A1012 SITE 5 AC3 21 HOH A1022 HOH A1096 DC B 112 DC C 204 SITE 6 AC3 21 DG C 205 SITE 1 AC4 6 HOH B 304 HOH B 305 HOH B 311 HOH B 313 SITE 2 AC4 6 HOH B 314 HOH C 430 SITE 1 AC5 2 DG C 213 DG C 214 SITE 1 AC6 6 DG C 205 HOH C 416 HOH C 422 HOH C 425 SITE 2 AC6 6 HOH C 426 HOH C 432 CRYST1 109.964 109.964 91.165 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009094 0.005250 0.000000 0.00000 SCALE2 0.000000 0.010501 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010969 0.00000